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PDBsum entry 1l2u
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protein Protein-protein interface(s) links
Lyase PDB id
1l2u

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
224 a.a. *
Waters ×121
* Residue conservation analysis
PDB id:
1l2u
Name: Lyase
Title: Orotidine 5'-monophosphate decarboxylase from e. Coli
Structure: Orotidine 5'-phosphate decarboxylase. Chain: a, b. Synonym: omp decarboxylase, ompdcase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.162     R-free:   0.211
Authors: P.Harris,J.C.Poulsen,K.F.Jensen,S.Larsen
Key ref:
P.Harris et al. (2002). Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase. J Mol Biol, 318, 1019-1029. PubMed id: 12054799 DOI: 10.1016/S0022-2836(02)00200-0
Date:
25-Feb-02     Release date:   13-Mar-02    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08244  (PYRF_ECOLI) -  Orotidine 5'-phosphate decarboxylase from Escherichia coli (strain K12)
Seq:
Struc: 		245 a.a.
224 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.23  - orotidine-5'-phosphate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Pyrimidine Biosynthesis
      Reaction: orotidine 5'-phosphate + H+ = UMP + CO2
orotidine 5'-phosphate
 + H(+)
 = UMP
 + CO2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00200-0 J Mol Biol 318:1019-1029 (2002)
PubMed id: 12054799  
 
 
Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase.
P.Harris, J.C.Poulsen, K.F.Jensen, S.Larsen.
 
  ABSTRACT  
 
Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate (UMP). We have earlier determined the structure of ODCase from Escherichia coli complexed with the inhibitor 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid (BMP); here we present the 2.5 A structure of the uncomplexed apo enzyme, determined from twinned crystals. A structural analysis and comparison of the two structures of the E. coli enzyme show that binding of the inhibitor is accompanied by significant domain movements of approximately 12 degrees around a hinge that crosses the active site. Hence, the ODCase dimer, which contains two active sites, may be divided in three domains: a central domain that is fixed, and two lids which independently move 12 degrees upon binding. Corresponding analyses, presented herein, of the two Saccharomyces cerevisiae ODCase structures (with and without BMP) and the Methanobacterium thermoautotrophicum ODCase structures (with and without 6-aza UMP) show very similar, but somewhat smaller domain movements. The domain movements seem to be initiated by the phosphoryl binding to the enzyme and can explain why the binding of the phosphoryl group is essential for the catalytic function.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Molscript figure of the domain movements in ODCase from E. coli caused by binding of the inhibitor BMP (shown in yellow). The complexed enzyme is shown in dark red, and domain I of the apo enzyme is shown in blue. Domain IIA of the apo enzyme is shown in green and domain IIB of the apo enzyme is shown in cyan. The rotation angles around the hinges (shown as arrows) are 12°. 		Figure 7.
Figure 7. The active site. The complexed structure is shown in red with the loop residues in bright red and the inhibitor BMP is shown in yellow. The apo structure is shown in blue.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1019-1029) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19618917 K.Toth, T.L.Amyes, B.M.Wood, K.K.Chan, J.A.Gerlt, and J.P.Richard (2009).
An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms.
  Biochemistry, 48, 8006-8013.  
17918849 K.Toth, T.L.Amyes, B.M.Wood, K.Chan, J.A.Gerlt, and J.P.Richard (2007).
Product deuterium isotope effect for orotidine 5'-monophosphate decarboxylase: evidence for the existence of a short-lived carbanion intermediate.
  J Am Chem Soc, 129, 12946-12947.  
16790931 R.C.Hillig, and L.Renault (2006).
Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.
  Acta Crystallogr D Biol Crystallogr, 62, 750-765.
PDB code: 2ca6
12777761 K.Houborg, P.Harris, J.C.Poulsen, P.Schneider, A.Svendsen, and S.Larsen (2003).
The structure of a mutant enzyme of Coprinus cinereus peroxidase provides an understanding of its increased thermostability.
  Acta Crystallogr D Biol Crystallogr, 59, 997.
PDB code: 1ly8
12777760 K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.Poulsen, P.Schneider, J.Vind, and S.Larsen (2003).
Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.
  Acta Crystallogr D Biol Crystallogr, 59, 989-996.
PDB codes: 1h3j 1ly9 1lyc 1lyk
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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